The log for the PDF -> EPUB is blank, despite the progress bar flashing through the various stages.
I've confirmed it does something similar for a mass conversion to FB2, this time with log cycling through 1209 sequential messages about converting CSS msostyles. I sensibly copied the text to the clipboard. Then promptly restarted the machine and booted into Windows. Oops.
I've also confirmed your own observation - the same books with the same operation in the same version of calibre don't error under Windows. PDF -> EPUB is a-okay under Win7 (using Unison to keep everything tidy).
Any thoughts as to what mught be tying up the last job, only under Linux?
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